def create_FORCE_SETS(interface_mode,
force_filenames,
symprec=1e-5,
is_wien2k_p1=False,
force_sets_zero_mode=False,
disp_filename='disp.yaml',
force_sets_filename='FORCE_SETS',
log_level=0):
if (interface_mode is None or interface_mode == 'vasp'
or interface_mode == 'pwmat' or interface_mode == 'abinit'
or interface_mode == 'elk' or interface_mode == 'pwscf'
or interface_mode == 'siesta' or interface_mode == 'crystal'):
disp_dataset = parse_disp_yaml(filename=disp_filename)
num_atoms = disp_dataset['natom']
num_displacements = len(disp_dataset['first_atoms'])
if force_sets_zero_mode:
num_displacements += 1
force_sets = get_force_sets(interface_mode,
num_atoms,
num_displacements,
force_filenames,
disp_filename,
verbose=(log_level > 0))
elif interface_mode == 'wien2k':
disp_dataset, supercell = parse_disp_yaml(filename=disp_filename,
return_cell=True)
from phonopy.interface.wien2k import parse_set_of_forces
num_displacements = len(disp_dataset['first_atoms'])
if force_sets_zero_mode:
num_displacements += 1
if _check_number_of_files(num_displacements, force_filenames,
disp_filename):
force_sets = []
else:
disps = [[d['number'], d['displacement']]
for d in disp_dataset['first_atoms']]
force_sets = parse_set_of_forces(disps,
force_filenames,
supercell,
is_distribute=(not is_wien2k_p1),
symprec=symprec,
verbose=(log_level > 0))
else:
force_sets = []
if force_sets:
if force_sets_zero_mode:
force_sets = _subtract_residual_forces(force_sets)
for forces, disp in zip(force_sets, disp_dataset['first_atoms']):
disp['forces'] = forces
write_FORCE_SETS(disp_dataset, filename=force_sets_filename)
if log_level > 0:
if force_sets:
print("%s has been created." % force_sets_filename)
else:
print("%s could not be created." % force_sets_filename)
return 0
def get_force_sets(interface_mode,
num_atoms,
num_displacements,
force_filenames,
disp_filename,
verbose=True):
if _check_number_of_files(num_displacements, force_filenames,
disp_filename):
return []
if interface_mode is None or interface_mode == 'vasp':
from phonopy.interface.vasp import parse_set_of_forces
elif interface_mode == 'pwmat':
from pwmat2phonopy.interface.pwmat import parse_set_of_forces
elif interface_mode == 'abinit':
from phonopy.interface.abinit import parse_set_of_forces
elif interface_mode == 'pwscf':
from phonopy.interface.pwscf import parse_set_of_forces
elif interface_mode == 'elk':
from phonopy.interface.elk import parse_set_of_forces
elif interface_mode == 'siesta':
from phonopy.interface.siesta import parse_set_of_forces
elif interface_mode == 'crystal':
from phonopy.interface.crystal import parse_set_of_forces
else:
return []
force_sets = parse_set_of_forces(num_atoms,
force_filenames,
verbose=verbose)
return force_sets
def get_force_sets(interface_mode,
num_atoms,
num_displacements,
force_filenames,
disp_filename,
verbose=True):
if _check_number_of_files(num_displacements,
force_filenames,
disp_filename):
return []
if interface_mode is None or interface_mode == 'vasp':
from phonopy.interface.vasp import parse_set_of_forces
elif interface_mode == 'abinit':
from phonopy.interface.abinit import parse_set_of_forces
elif interface_mode == 'pwscf':
from phonopy.interface.pwscf import parse_set_of_forces
elif interface_mode == 'elk':
from phonopy.interface.elk import parse_set_of_forces
elif interface_mode == 'siesta':
from phonopy.interface.siesta import parse_set_of_forces
else:
return []
force_sets = parse_set_of_forces(num_atoms,
force_filenames,
verbose=verbose)
return force_sets
def get_force_sets(interface_mode, num_atoms, force_filenames):
if interface_mode is None or interface_mode == 'vasp':
from phonopy.interface.vasp import parse_set_of_forces
force_sets = parse_set_of_forces(num_atoms, force_filenames)
elif interface_mode == 'abinit':
from phonopy.interface.abinit import parse_set_of_forces
force_sets = parse_set_of_forces(num_atoms, force_filenames)
elif interface_mode == 'pwscf':
from phonopy.interface.pwscf import parse_set_of_forces
force_sets = parse_set_of_forces(num_atoms, force_filenames)
elif interface_mode == 'elk':
from phonopy.interface.elk import parse_set_of_forces
force_sets = parse_set_of_forces(num_atoms, force_filenames)
elif interface_mode == 'siesta':
from phonopy.interface.siesta import parse_set_of_forces
force_sets = parse_set_of_forces(num_atoms, force_filenames)
return force_sets
def get_force_sets(interface_mode, num_atoms, force_filenames):
if interface_mode is None or interface_mode == 'vasp':
from phonopy.interface.vasp import parse_set_of_forces
force_sets = parse_set_of_forces(num_atoms, force_filenames)
elif interface_mode == 'abinit':
from phonopy.interface.abinit import parse_set_of_forces
force_sets = parse_set_of_forces(num_atoms, force_filenames)
elif interface_mode == 'pwscf':
from phonopy.interface.pwscf import parse_set_of_forces
force_sets = parse_set_of_forces(num_atoms, force_filenames)
elif interface_mode == 'elk':
from phonopy.interface.elk import parse_set_of_forces
force_sets = parse_set_of_forces(num_atoms, force_filenames)
elif interface_mode == 'siesta':
from phonopy.interface.siesta import parse_set_of_forces
force_sets = parse_set_of_forces(num_atoms, force_filenames)
return force_sets
def create_FORCE_SETS(interface_mode,
force_filenames,
symprec,
is_wien2k_p1=False,
force_sets_zero_mode=False,
log_level=0):
if (interface_mode is None or
interface_mode == 'vasp' or
interface_mode == 'abinit' or
interface_mode == 'elk' or
interface_mode == 'pwscf' or
interface_mode == 'siesta'):
displacements = parse_disp_yaml(filename='disp.yaml')
num_atoms = displacements['natom']
if _check_number_of_files(displacements,
force_filenames,
force_sets_zero_mode):
return 1
force_sets = _get_force_sets(interface_mode, num_atoms, force_filenames)
elif interface_mode == 'wien2k':
displacements, supercell = parse_disp_yaml(filename='disp.yaml',
return_cell=True)
from phonopy.interface.wien2k import parse_set_of_forces
if _check_number_of_files(displacements,
force_filenames,
force_sets_zero_mode):
return 1
force_sets = parse_set_of_forces(
displacements,
force_filenames,
supercell,
disp_keyword='first_atoms',
is_distribute=(not is_wien2k_p1),
symprec=symprec)
else:
force_sets = []
if force_sets:
if force_sets_zero_mode:
force_sets = _subtract_residual_forces(force_sets)
for forces, disp in zip(force_sets, displacements['first_atoms']):
disp['forces'] = forces
write_FORCE_SETS(displacements, filename='FORCE_SETS')
if log_level > 0:
if force_sets:
print("FORCE_SETS has been created.")
else:
print("FORCE_SETS could not be created.")
return 0
def create_FORCE_SETS(interface_mode,
force_filenames,
symprec,
is_wien2k_p1=False,
log_level=0):
if (interface_mode is None or
interface_mode == 'vasp' or
interface_mode == 'abinit' or
interface_mode == 'elk' or
interface_mode == 'pwscf' or
interface_mode == 'siesta'):
displacements = parse_disp_yaml(filename='disp.yaml')
num_atoms = displacements['natom']
if len(displacements['first_atoms']) != len(force_filenames):
print('')
print("Number of files to be read don't match "
"to number of displacements in disp.yaml.")
return 1
force_sets = get_force_sets(interface_mode, num_atoms, force_filenames)
elif interface_mode == 'wien2k':
displacements, supercell = parse_disp_yaml(filename='disp.yaml',
return_cell=True)
if len(displacements['first_atoms']) != len(force_filenames):
print('')
print("Number of files to be read don't match "
"to number of displacements in disp.yaml.")
return 1
from phonopy.interface.wien2k import parse_set_of_forces
force_sets = parse_set_of_forces(
displacements,
force_filenames,
supercell,
disp_keyword='first_atoms',
is_distribute=(not is_wien2k_p1),
symprec=symprec)
else:
force_sets = []
if force_sets:
for forces, disp in zip(force_sets, displacements['first_atoms']):
disp['forces'] = forces
write_FORCE_SETS(displacements, filename='FORCE_SETS')
if log_level > 0:
if force_sets:
print("FORCE_SETS has been created.")
else:
print("FORCE_SETS could not be created.")
return 0
def create_FORCE_SETS(interface_mode,
force_filenames,
options,
log_level=0):
if (interface_mode == 'vasp' or
interface_mode == 'abinit' or
interface_mode == 'elk' or
interface_mode == 'pwscf' or
interface_mode == 'siesta'):
displacements = parse_disp_yaml(filename='disp.yaml')
num_atoms = displacements['natom']
if len(displacements['first_atoms']) != len(force_filenames):
print('')
print("Number of files to be read don't match "
"to number of displacements in disp.yaml.")
return 1
force_sets = get_force_sets(interface_mode, num_atoms, force_filenames)
elif interface_mode == 'wien2k':
displacements, supercell = parse_disp_yaml(filename='disp.yaml',
return_cell=True)
if len(displacements['first_atoms']) != len(force_filenames):
print('')
print("Number of files to be read don't match "
"to number of displacements in disp.yaml.")
return 1
from phonopy.interface.wien2k import parse_set_of_forces
force_sets = parse_set_of_forces(
displacements,
force_filenames,
supercell,
disp_keyword='first_atoms',
is_distribute=(not options.is_wien2k_p1),
symprec=options.symprec)
else:
force_sets = []
if force_sets:
for forces, disp in zip(force_sets, displacements['first_atoms']):
disp['forces'] = forces
write_FORCE_SETS(displacements, filename='FORCE_SETS')
if log_level > 0:
if force_sets:
print("FORCE_SETS has been created.")
else:
print("FORCE_SETS could not be created.")
return 0
def get_force_sets(interface_mode,
num_atoms,
num_displacements,
force_filenames,
disp_filename=None,
check_number_of_files=False,
verbose=True):
if check_number_of_files:
if _check_number_of_files(num_displacements,
force_filenames,
disp_filename):
return []
if interface_mode is None or interface_mode == 'vasp':
from phonopy.interface.vasp import parse_set_of_forces
elif interface_mode == 'abinit':
from phonopy.interface.abinit import parse_set_of_forces
elif interface_mode == 'qe':
from phonopy.interface.qe import parse_set_of_forces
elif interface_mode == 'elk':
from phonopy.interface.elk import parse_set_of_forces
elif interface_mode == 'siesta':
from phonopy.interface.siesta import parse_set_of_forces
elif interface_mode == 'cp2k':
from phonopy.interface.cp2k import parse_set_of_forces
elif interface_mode == 'crystal':
from phonopy.interface.crystal import parse_set_of_forces
elif interface_mode == 'dftbp':
from phonopy.interface.dftbp import parse_set_of_forces
elif interface_mode == 'turbomole':
from phonopy.interface.turbomole import parse_set_of_forces
else:
return []
force_sets = parse_set_of_forces(num_atoms,
force_filenames,
verbose=verbose)
return force_sets
def create_FORCE_SETS(interface_mode,
force_filenames,
symmetry_tolerance=None,
is_wien2k_p1=False,
force_sets_zero_mode=False,
disp_filename='disp.yaml',
force_sets_filename='FORCE_SETS',
log_level=0):
if log_level > 0:
if interface_mode:
print("Calculator interface: %s" % interface_mode)
print("Displacements were read from \"%s\"." % disp_filename)
if disp_filename == 'disp.yaml':
print('')
print("NOTE:")
print(" From phonopy v2.0, displacements are written into "
"\"phonopy_disp.yaml\".")
print(" \"disp.yaml\" is still supported for reading, but is "
"deprecated.")
print('')
if force_sets_zero_mode:
print("Forces in %s are subtracted from forces in all "
"other files." % force_filenames[0])
if disp_filename == 'disp.yaml':
disp_dataset, supercell = parse_disp_yaml(filename=disp_filename,
return_cell=True)
else:
phpy = PhonopyYaml()
phpy.read(disp_filename)
supercell = phpy.supercell
disp_dataset = phpy.dataset
if 'natom' in disp_dataset: # type-1 dataset
num_atoms = disp_dataset['natom']
num_displacements = len(disp_dataset['first_atoms'])
dataset_type = 1
elif 'displacements' in disp_dataset: # type-2 dataset
num_atoms = disp_dataset['displacements'].shape[1]
num_displacements = disp_dataset['displacements'].shape[0]
dataset_type = 2
else:
raise RuntimeError("Number of atoms could not be retrieved from %s" %
disp_filename)
if force_sets_zero_mode:
num_displacements += 1
if interface_mode in (None, 'vasp', 'abinit', 'elk', 'qe', 'siesta',
'cp2k', 'crystal', 'dftbp', 'turbomole'):
force_sets = get_force_sets(interface_mode,
num_atoms,
num_displacements,
force_filenames,
disp_filename=disp_filename,
check_number_of_files=True,
verbose=(log_level > 0))
elif interface_mode == 'wien2k':
from phonopy.interface.wien2k import parse_set_of_forces
if not _check_number_of_files(num_displacements, force_filenames,
disp_filename):
force_sets = []
else:
disps, _ = get_displacements_and_forces(disp_dataset)
force_sets = parse_set_of_forces(
disps,
force_filenames,
supercell,
is_distribute=(not is_wien2k_p1),
symmetry_tolerance=symmetry_tolerance,
verbose=(log_level > 0))
else:
force_sets = []
if force_sets:
if force_sets_zero_mode:
force_sets = _subtract_residual_forces(force_sets)
if dataset_type == 1:
for forces, disp in zip(force_sets, disp_dataset['first_atoms']):
disp['forces'] = forces
elif dataset_type == 2:
disp_dataset['forces'] = np.array(force_sets,
dtype='double',
order='C')
else:
raise RuntimeError("FORCE_SETS could not be created.")
write_FORCE_SETS(disp_dataset, filename=force_sets_filename)
if log_level > 0:
if force_sets:
print("%s has been created." % force_sets_filename)
else:
print("%s could not be created." % force_sets_filename)
return 0
def create_FORCE_SETS(interface_mode,
force_filenames,
symmetry_tolerance=None,
is_wien2k_p1=False,
force_sets_zero_mode=False,
disp_filename='disp.yaml',
force_sets_filename='FORCE_SETS',
log_level=0):
if log_level > 0:
if interface_mode:
print("Calculator interface: %s" % interface_mode)
print("Displacements were read from \"%s\"." % disp_filename)
if disp_filename == 'disp.yaml':
print('')
print("NOTE:")
print(" From phonopy v2.0, displacements are written into "
"\"phonopy_disp.yaml\".")
print(" \"disp.yaml\" is still supported for reading, but is "
"deprecated.")
print('')
if force_sets_zero_mode:
print("Forces in %s are subtracted from forces in all "
"other files." % force_filenames[0])
if interface_mode in (None, 'vasp', 'abinit', 'elk', 'qe', 'siesta',
'cp2k', 'crystal', 'dftbp', 'turbomole'):
disp_dataset = parse_disp_yaml(filename=disp_filename)
num_atoms = disp_dataset['natom']
num_displacements = len(disp_dataset['first_atoms'])
if force_sets_zero_mode:
num_displacements += 1
force_sets = get_force_sets(interface_mode,
num_atoms,
num_displacements,
force_filenames,
disp_filename=disp_filename,
check_number_of_files=True,
verbose=(log_level > 0))
elif interface_mode == 'wien2k':
disp_dataset, supercell = parse_disp_yaml(filename=disp_filename,
return_cell=True)
from phonopy.interface.wien2k import parse_set_of_forces
num_displacements = len(disp_dataset['first_atoms'])
if force_sets_zero_mode:
num_displacements += 1
if _check_number_of_files(num_displacements,
force_filenames,
disp_filename):
force_sets = []
else:
disps = [[d['number'], d['displacement']]
for d in disp_dataset['first_atoms']]
force_sets = parse_set_of_forces(
disps,
force_filenames,
supercell,
is_distribute=(not is_wien2k_p1),
symmetry_tolerance=symmetry_tolerance,
verbose=(log_level > 0))
else:
force_sets = []
if force_sets:
if force_sets_zero_mode:
force_sets = _subtract_residual_forces(force_sets)
for forces, disp in zip(force_sets, disp_dataset['first_atoms']):
disp['forces'] = forces
write_FORCE_SETS(disp_dataset, filename=force_sets_filename)
if log_level > 0:
if force_sets:
print("%s has been created." % force_sets_filename)
else:
print("%s could not be created." % force_sets_filename)
return 0
def create_FORCE_SETS(interface_mode,
force_filenames,
symprec=1e-5,
is_wien2k_p1=False,
force_sets_zero_mode=False,
disp_filename='disp.yaml',
force_sets_filename='FORCE_SETS',
log_level=0):
if (interface_mode is None or
interface_mode == 'vasp' or
interface_mode == 'abinit' or
interface_mode == 'elk' or
interface_mode == 'lmto' or
interface_mode == 'qe' or
interface_mode == 'siesta' or
interface_mode == 'cp2k' or
interface_mode == 'crystal'):
disp_dataset = parse_disp_yaml(filename=disp_filename)
num_atoms = disp_dataset['natom']
num_displacements = len(disp_dataset['first_atoms'])
if force_sets_zero_mode:
num_displacements += 1
force_sets = get_force_sets(interface_mode,
num_atoms,
num_displacements,
force_filenames,
disp_filename,
verbose=(log_level > 0))
elif interface_mode == 'wien2k':
disp_dataset, supercell = parse_disp_yaml(filename=disp_filename,
return_cell=True)
from phonopy.interface.wien2k import parse_set_of_forces
num_displacements = len(disp_dataset['first_atoms'])
if force_sets_zero_mode:
num_displacements += 1
if _check_number_of_files(num_displacements,
force_filenames,
disp_filename):
force_sets = []
else:
disps = [[d['number'], d['displacement']]
for d in disp_dataset['first_atoms']]
force_sets = parse_set_of_forces(
disps,
force_filenames,
supercell,
is_distribute=(not is_wien2k_p1),
symprec=symprec,
verbose=(log_level > 0))
else:
force_sets = []
if force_sets:
if force_sets_zero_mode:
force_sets = _subtract_residual_forces(force_sets)
for forces, disp in zip(force_sets, disp_dataset['first_atoms']):
disp['forces'] = forces
write_FORCE_SETS(disp_dataset, filename=force_sets_filename)
if log_level > 0:
if force_sets:
print("%s has been created." % force_sets_filename)
else:
print("%s could not be created." % force_sets_filename)
return 0
